k.test {KODAMA}R Documentation

K-Test of Statistical Association

Description

This function performs a permutation test using PLS to assess association between the KODAMA output and any additional related parameters such as clinical metadata.

Usage

k.test(data, labels, n = 100)

Arguments

data

a matrix.

labels

a classification vector.

n

number of iterations of the permutation test.

Value

The p-value of the test.

Author(s)

Stefano Cacciatore

References

Cacciatore S, Luchinat C, Tenori L
Knowledge discovery by accuracy maximization.
Proc Natl Acad Sci U S A 2014;111(14):5117-22. doi: 10.1073/pnas.1220873111. Link

Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA
KODAMA: an updated R package for knowledge discovery and data mining.
Bioinformatics 2017;33(4):621-623. doi: 10.1093/bioinformatics/btw705. Link

See Also

KODAMA

Examples

# data(iris)
# data=iris[,-5]
# labels=iris[,5]
# kk=KODAMA(data,FUN="PLS-DA")
# kkplot=kk$pp
# k1=k.test(kkplot,labels)
# print(k1)
# k2=k.test(kkplot,sample(labels))
# print(k2)

[Package KODAMA version 1.5 Index]